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These tutorials explain steps that are used to analyze real-world sequencing data. We will try to explain the steps in detail but command output are usually ignored for brevity and confidentiality reasons.
This is a 10-minute quick start guide using data from the 1000 genomes project. We encourage you to walk through this minimal real-world example to get a feel for the software and assess its helpfulness.
- A recent presentation about variant tools, with output of commands
- A tutorial session in the ACM BCB 2014 meeting
- Analyzing 44 whole genome cases and 200 exome controls, with detailed performance measures
- Analyzing 5 whole-genome samples from Illumina
- Compare variants from the same samples called by Complete Genomics and Illumina
- Select variants belonging to specified genes
- Detailed analysis of one variant
- Import all genotype data from the 1000 genomes project
- Generate and import annovar annotations for variants already in vtools
- Import variants from a list of variants in an unsupported format
- Handling genotypes imported from multiple files (e.g. genotypes of samples are imported chromosome by chromosome)